The ubiX gene of Colwellia psychrerythraea strain 34H encodes a 3-octaprenyl-4-hydroxybenzoate carboxylase (CpsUbiX, UniProtKB code: Q489U8) that is involved in the third step of the ubiquinone biosynthesis pathway and uses flavin mononucleotide (FMN) as a cofactor. Here, we report the crystal structures of two forms of CpsUbiX: an FMN-bound wild type form and an FMN-unbound V47S mutant form. CpsUbiX is a dodecameric enzyme, and each monomer possesses a typical Rossmann-fold structure. However, to our knowledge, the architecture of the FMN-binding domain formed by three neighboring subunits described here is novel and unique to UbiX. The highly conserved Gly15, Ser41, Val47, and Tyr171 residues play important roles in FMN binding. Structural comparison of the FMN-bound wild type form with the FMN-free form revealed a significant conformational difference in the C-terminal loop region (comprising residues 170–177 and 195–206). Subsequent computational modeling and liposome binding assay both suggested that the conformational change observed in the C-terminal loops upon FMN binding plays an important role in substrate binding. The crystal structures presented in this work provide structural framework and insights into the catalytic mechanism of CpsUbiX. To investigate FMN binding mechanism, we have carried out structural studies. As the first step toward its structural elucidation, we report the results of preliminary X-ray crystallographic experiments with CpsUbiX with or without (V47S) cofactor FMN.